IDEAS home Printed from https://ideas.repec.org/a/nat/natcom/v14y2023i1d10.1038_s41467-023-43867-y.html
   My bibliography  Save this article

Resin acids play key roles in shaping microbial communities during degradation of spruce bark

Author

Listed:
  • Amanda Sörensen Ristinmaa

    (Chalmers University of Technology)

  • Albert Tafur Rangel

    (Chalmers University of Technology
    Technical University of Denmark)

  • Alexander Idström

    (Chalmers University of Technology)

  • Sebastian Valenzuela

    (University of Gothenburg)

  • Eduard J. Kerkhoven

    (Chalmers University of Technology
    Technical University of Denmark)

  • Phillip B. Pope

    (Norwegian University of Life Sciences
    Biotechnology and Food Science, Norwegian University of Life Sciences)

  • Merima Hasani

    (Chalmers University of Technology
    Chalmers University of Technology)

  • Johan Larsbrink

    (Chalmers University of Technology
    Chalmers University of Technology)

Abstract

The bark is the outermost defense of trees against microbial attack, largely thanks to toxicity and prevalence of extractive compounds. Nevertheless, bark decomposes in nature, though by which species and mechanisms remains unknown. Here, we have followed the development of microbial enrichments growing on spruce bark over six months, by monitoring both chemical changes in the material and performing community and metagenomic analyses. Carbohydrate metabolism was unexpectedly limited, and instead a key activity was metabolism of extractives. Resin acid degradation was principally linked to community diversification with specific bacteria revealed to dominate the process. Metagenome-guided isolation facilitated the recovery of the dominant enrichment strain in pure culture, which represents a new species (Pseudomonas abieticivorans sp. nov.), that can grow on resin acids as a sole carbon source. Our results illuminate key stages in degradation of an abundant renewable resource, and how defensive extractive compounds have major roles in shaping microbiomes.

Suggested Citation

  • Amanda Sörensen Ristinmaa & Albert Tafur Rangel & Alexander Idström & Sebastian Valenzuela & Eduard J. Kerkhoven & Phillip B. Pope & Merima Hasani & Johan Larsbrink, 2023. "Resin acids play key roles in shaping microbial communities during degradation of spruce bark," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
  • Handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43867-y
    DOI: 10.1038/s41467-023-43867-y
    as

    Download full text from publisher

    File URL: https://www.nature.com/articles/s41467-023-43867-y
    File Function: Abstract
    Download Restriction: no

    File URL: https://libkey.io/10.1038/s41467-023-43867-y?utm_source=ideas
    LibKey link: if access is restricted and if your library uses this service, LibKey will redirect you to where you can use your library subscription to access this item
    ---><---

    References listed on IDEAS

    as
    1. Mads Albertsen & Søren M Karst & Anja S Ziegler & Rasmus H Kirkegaard & Per H Nielsen, 2015. "Back to Basics – The Influence of DNA Extraction and Primer Choice on Phylogenetic Analysis of Activated Sludge Communities," PLOS ONE, Public Library of Science, vol. 10(7), pages 1-15, July.
    2. Luke C. Jeffrey & Damien T. Maher & Eleonora Chiri & Pok Man Leung & Philipp A. Nauer & Stefan K. Arndt & Douglas R. Tait & Chris Greening & Scott G. Johnston, 2021. "Bark-dwelling methanotrophic bacteria decrease methane emissions from trees," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
    3. Peter Menzel & Kim Lee Ng & Anders Krogh, 2016. "Fast and sensitive taxonomic classification for metagenomics with Kaiju," Nature Communications, Nature, vol. 7(1), pages 1-9, September.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Sposób, Michał, 2024. "Optimization of ex-situ biomethanation process in trickle bed reactor: The impact of slight H2/CO2 ratio adjustments and different packing materials," Renewable Energy, Elsevier, vol. 222(C).
    2. Hagger, Valerie & Waltham, Nathan J. & Lovelock, Catherine E., 2022. "Opportunities for coastal wetland restoration for blue carbon with co-benefits for biodiversity, coastal fisheries, and water quality," Ecosystem Services, Elsevier, vol. 55(C).
    3. Peng Liu & Jessica Ewald & Zhiqiang Pang & Elena Legrand & Yeon Seon Jeon & Jonathan Sangiovanni & Orcun Hacariz & Guangyan Zhou & Jessica A. Head & Niladri Basu & Jianguo Xia, 2023. "ExpressAnalyst: A unified platform for RNA-sequencing analysis in non-model species," Nature Communications, Nature, vol. 14(1), pages 1-11, December.
    4. Wei Ding & Shougang Wang & Peng Qin & Shen Fan & Xiaoyan Su & Peiyan Cai & Jie Lu & Han Cui & Meng Wang & Yi Shu & Yongming Wang & Hui-Hui Fu & Yu-Zhong Zhang & Yong-Xin Li & Weipeng Zhang, 2023. "Anaerobic thiosulfate oxidation by the Roseobacter group is prevalent in marine biofilms," Nature Communications, Nature, vol. 14(1), pages 1-14, December.
    5. Daniela S. Aliaga Goltsman & Lisa M. Alexander & Jyun-Liang Lin & Rodrigo Fregoso Ocampo & Benjamin Freeman & Rebecca C. Lamothe & Andres Perez Rivas & Morayma M. Temoche-Diaz & Shailaja Chadha & Nata, 2022. "Compact Cas9d and HEARO enzymes for genome editing discovered from uncultivated microbes," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    6. Ernestina Hauptfeld & Nikolaos Pappas & Sandra Iwaarden & Basten L. Snoek & Andrea Aldas-Vargas & Bas E. Dutilh & F. A. Bastiaan Meijenfeldt, 2024. "Integrating taxonomic signals from MAGs and contigs improves read annotation and taxonomic profiling of metagenomes," Nature Communications, Nature, vol. 15(1), pages 1-12, December.
    7. Dhuha Sulaiman Salim Al-Daghari & Abdullah Mohammed Al-Sadi & Issa Hashil Al-Mahmooli & Rhonda Janke & Rethinasamy Velazhahan, 2023. "Biological Control Efficacy of Indigenous Antagonistic Bacteria Isolated from the Rhizosphere of Cabbage Grown in Biofumigated Soil against Pythium aphanidermatum Damping-Off of Cucumber," Agriculture, MDPI, vol. 13(3), pages 1-20, March.
    8. J. L. Rolando & M. Kolton & T. Song & Y. Liu & P. Pinamang & R. Conrad & J. T. Morris & K. T. Konstantinidis & J. E. Kostka, 2024. "Sulfur oxidation and reduction are coupled to nitrogen fixation in the roots of the salt marsh foundation plant Spartina alterniflora," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    9. Omary Mzava & Alexandre Pellan Cheng & Adrienne Chang & Sami Smalling & Liz-Audrey Kounatse Djomnang & Joan Sesing Lenz & Randy Longman & Amy Steadman & Luis G. Gómez-Escobar & Edward J. Schenck & Mir, 2022. "A metagenomic DNA sequencing assay that is robust against environmental DNA contamination," Nature Communications, Nature, vol. 13(1), pages 1-10, December.
    10. Lharbi Dridi & Fernando Altamura & Emmanuel Gonzalez & Olivia Lui & Ryszard Kubinski & Reilly Pidgeon & Adrian Montagut & Jasmine Chong & Jianguo Xia & Corinne F. Maurice & Bastien Castagner, 2023. "Identifying glycan consumers in human gut microbiota samples using metabolic labeling coupled with fluorescence-activated cell sorting," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    11. Alexa M. Nicolas & Ella T. Sieradzki & Jennifer Pett-Ridge & Jillian F. Banfield & Michiko E. Taga & Mary K. Firestone & Steven J. Blazewicz, 2023. "A subset of viruses thrives following microbial resuscitation during rewetting of a seasonally dry California grassland soil," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    12. Márk Szuhaj & Roland Wirth & Zoltán Bagi & Gergely Maróti & Gábor Rákhely & Kornél L. Kovács, 2021. "Development of Stable Mixed Microbiota for High Yield Power to Methane Conversion," Energies, MDPI, vol. 14(21), pages 1-17, November.
    13. Minh Nguyen Quang & Tim Rogers & Jan Hofman & Ana B Lanham, 2019. "New framework for automated article selection applied to a literature review of Enhanced Biological Phosphorus Removal," PLOS ONE, Public Library of Science, vol. 14(5), pages 1-42, May.
    14. Louise B. Sennett & Constance A. Roco & Natalie Y. N. Lim & Joseph B. Yavitt & Peter Dörsch & Lars R. Bakken & James P. Shapleigh & Åsa Frostegård, 2024. "Determining how oxygen legacy affects trajectories of soil denitrifier community dynamics and N2O emissions," Nature Communications, Nature, vol. 15(1), pages 1-13, December.
    15. Manoshi S. Datta & Idan Yelin & Ori Hochwald & Imad Kassis & Liron Borenstein-Levin & Amir Kugelman & Roy Kishony, 2021. "Rapid methicillin resistance diversification in Staphylococcus epidermidis colonizing human neonates," Nature Communications, Nature, vol. 12(1), pages 1-10, December.
    16. Heleen T. Ouboter & Rob Mesman & Tom Sleutels & Jelle Postma & Martijn Wissink & Mike S. M. Jetten & Annemiek Ter Heijne & Tom Berben & Cornelia U. Welte, 2024. "Mechanisms of extracellular electron transfer in anaerobic methanotrophic archaea," Nature Communications, Nature, vol. 15(1), pages 1-11, December.
    17. Mason. R. Stothart & Philip. D. McLoughlin & Sarah. A. Medill & Ruth. J. Greuel & Alastair. J. Wilson & Jocelyn. Poissant, 2024. "Methanogenic patterns in the gut microbiome are associated with survival in a population of feral horses," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    18. Zheng Sun & Jiang Liu & Meng Zhang & Tong Wang & Shi Huang & Scott T. Weiss & Yang-Yu Liu, 2023. "Removal of false positives in metagenomics-based taxonomy profiling via targeting Type IIB restriction sites," Nature Communications, Nature, vol. 14(1), pages 1-12, December.
    19. Kaiyuan Zhu & Alejandro A. Schäffer & Welles Robinson & Junyan Xu & Eytan Ruppin & A. Funda Ergun & Yuzhen Ye & S. Cenk Sahinalp, 2022. "Strain level microbial detection and quantification with applications to single cell metagenomics," Nature Communications, Nature, vol. 13(1), pages 1-19, December.
    20. Marc Schoeler & Sandrine Ellero-Simatos & Till Birkner & Jordi Mayneris-Perxachs & Lisa Olsson & Harald Brolin & Ulrike Loeber & Jamie D. Kraft & Arnaud Polizzi & Marian Martí-Navas & Josep Puig & Ant, 2023. "The interplay between dietary fatty acids and gut microbiota influences host metabolism and hepatic steatosis," Nature Communications, Nature, vol. 14(1), pages 1-16, December.

    More about this item

    Statistics

    Access and download statistics

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:nat:natcom:v:14:y:2023:i:1:d:10.1038_s41467-023-43867-y. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: Sonal Shukla or Springer Nature Abstracting and Indexing (email available below). General contact details of provider: http://www.nature.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.